Corals from the Gulf of Aqaba (northern Red Sea) are resilient to high temperatures and therefore this region is regarded as globally important for reef conservation. However, long-term dynamics of coral reef assemblages from the Gulf of Aqaba remain largely understudied. In this study, we analysed the change in benthic, fish and invertebrate assemblages of reefs around Dahab (South Sinai, Egypt) between 2009 and 2019. We also studied the individual trajectories of coral reef benthic categories, key invertebrate and fish species and their relationship. As site emerged as the main factor explaining the variability in coral reef communities, we identified three clusters of sites with similar assemblages. Both benthic, fish and invertebrate assemblages changed considerably at the three site clusters between 2009 and 2019. We found significant increases in fleshy macroalgae (~ 6 to 15%) and cyanobacterial mats (~ 6 to 12%) in all site clusters. Although not observing a significant reduction of hard coral cover, both macroalgae mat cover and cyanobacterial mat cover were significantly negatively related to hard coral cover and hard coral disease. Soft coral cover (mainly corals from the Xeniidae family) decreased significantly in two of the site clusters, their cover being negatively related to macroalgal and cyanobacterial cover. Significant declines in grazer urchins were observed at all site clusters, and a strong negative relationship was found with macroalgae and cyanobacterial mats cover, suggesting urchin decline as one of the main drivers behind algal increases. Different site clusters had different fish trajectories (butterflyfish, parrotfish, surgeonfish and predators), with only damselfish densities significantly decreasing at all sites. A significant decrease in damselfish densities was related to increases in cyanobacterial mats. These findings suggest that if macroalgae and cyanobacteria continue to increase, Dahab coral reefs could undergo degradation, and therefore, more studies are needed to elucidate the drivers behind these algal increases.